full wwpdb x-ray structure validation report i · ramachandranoutliers 120053 1013(2.78-2.74)...

Full wwPDB X-ray Structure Validation Report iO

Aug 10, 2020 � 01:45 AM BST

PDB ID : 1A6ATitle : THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATU-

RATION: CLIP BOUND TO HLA-DR3Authors : Ghosh, P.; Amaya, M.; Mellins, E.; Wiley, D.C.

Deposited on : 1998-02-22Resolution : 2.75 Å(reported)

This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected] user guide is available at

https://www.wwpdb.org/validation/2017/XrayValidationReportHelpwith speci�c help available everywhere you see the iO symbol.

The following versions of software and data (see references iO) were used in the production of this report:

MolProbity : 4.02b-467Mogul : 1.8.5 (274361), CSD as541be (2020)

Xtriage (Phenix) : 1.13EDS : 2.13.1

Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Refmac : 5.8.0158CCP4 : 7.0.044 (Gargrove)

Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et al. (1996)

Validation Pipeline (wwPDB-VP) : 2.13.1

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp



https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#references

Full wwPDB X-ray Structure Validation Report 1A6A

1 Overall quality at a glance iO

The following experimental techniques were used to determine the structure:X-RAY DIFFRACTION

The reported resolution of this entry is 2.75 Å.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

MetricWhole archive(#Entries)

Similar resolution(#Entries, resolution range(Å))

Rfree 130704 1235 (2.78-2.74)Clashscore 141614 1277 (2.78-2.74)

Ramachandran outliers 138981 1257 (2.78-2.74)Sidechain outliers 138945 1257 (2.78-2.74)RSRZ outliers 127900 1207 (2.78-2.74)

The table below summarises the geometric issues observed across the polymeric chains and their�t to the electron density. The red, orange, yellow and green segments on the lower bar indicatethe fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric qualitycriteria respectively. A grey segment represents the fraction of residues that are not modelled.The numeric value for each fraction is indicated below the corresponding segment, with a dotrepresenting fractions <=5% The upper red bar (where present) indicates the fraction of residuesthat have poor �t to the electron density. The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 176

2 B 187

3 C 15

The following table lists non-polymeric compounds, carbohydrate monomers and non-standardresidues in protein, DNA, RNA chains that are outliers for geometric or electron-density-�t crite-ria:

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#overall_quality


Mol Type Chain Res Chirality Geometry Clashes Electron density4 NAG A 181 - - - X4 NAG A 200 - - - X


2 Entry composition iO

There are 5 unique types of molecules in this entry. The entry contains 3158 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occu-pancy, the AltConf column contains the number of residues with at least one atom in alternateconformation and the Trace column contains the number of residues modelled with at most 2atoms.

� Molecule 1 is a protein called HLA class II histocompatibility antigen, DR alpha chain.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 176Total C N O S1447 940 236 266 5

6 0 0

� Molecule 2 is a protein called HLA class II histocompatibility antigen, DR-1 beta chain.


2 B 187Total C N O S1548 973 281 289 5

60 0 0

� Molecule 3 is a protein called HLA class II histocompatibility antigen, gamma chain.


3 C 15Total C N O S113 72 20 18 3

0 0 0

� Molecule 4 is 2-acetamido-2-deoxy-beta-D-glucopyranose (three-letter code: NAG) (formula:C8H15NO6).

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#entry_composition


Mol Chain Residues Atoms ZeroOcc AltConf

4 A 1Total C N O14 8 1 5

0 0

4 A 1Total C N O14 8 1 5

0 0

� Molecule 5 is water.

Mol Chain Residues Atoms ZeroOcc AltConf

5 A 8Total O8 8

0 0

5 B 13Total O13 13

0 0

5 C 1Total O1 1

0 0


3 Residue-property plots iO

These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The�rst graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andelectron density. Residues are color-coded according to the number of geometric quality criteriafor which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more.A red dot above a residue indicates a poor �t to the electron density (RSRZ > 2). Stretches of 2or more consecutive residues without any outlier are shown as a green connector. Residues presentin the sample, but not in the model, are shown in grey.

• Molecule 1: HLA class II histocompatibility antigen, DR alpha chain

Chain A:

H5

V6

I7

I8

Q9

A10

E11

L14

N15

P16

E21

F22

M23

F24

D25

F26

V34

K38•

K39

L45

E46

E47

F48

G49

R50

F51

A52

S53

G58

A59

L60

A61

A64

V65

D66

K67

L70

E71

K75

Y79

T83

P87

V91

L92

T93

N94

S95

P96

R100•

E101•

P102

N103

V104

L105

F108

I109

D110

K111

F112

T113

P114

P115

V116

V117

N118

V119

T120

W121

K126•

P127

V128

T129•

T130•

S133

E134

T135

V136

F137

R140

E141•

F145

R146

K147

F148

H149

Y150

F153

Y161

D162

C163•

R164

V165

E166

H167

W168

D171•

E172•

P173

L174

L175

K176

H177

W178

E179

F180•

• Molecule 2: HLA class II histocompatibility antigen, DR-1 beta chain

Chain B:

P5

R6

F7

L8

T12

S13

E14

C15

H16

F17

F18•

N19•

G20

T21

V24

R25

Y26

L27

D28

R29

Y30

F31

H32

N33

Q34

E35

E36

N37

V38

R39

F40

D41

V44

A49

V50

T51

E52

R55

P56

D57

A58

W61

N62

D66

L67

L68

E69

Q70

K71

R72

G73

R74

V75

D76

N77

Y78

C79

R80

H81

N82

V85

V86

E87

S88

F89

T90

V91

R94

V95

H96

P97

K105•

T106•

Q107•

P108•

L109•

H112•

V116

S120

G121

F122

I127

E128

V129

R130

W131

N134•

E137

E138

K139

T140

G141

S144

Q156

V159

M160

L161

E162

T163

V164

P165

R166

S167•

G168

E169

V170•

Y171

T172

C173

Q174

V175

E176

H177

P178

S179

V180

P183

L184

T185

V186

E187

R191

• Molecule 3: HLA class II histocompatibility antigen, gamma chain

Chain C:

P87•

K90

M91

R92

M93

A94

T95

P96

L97

A101

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#residue_plots


4 Data and re�nement statistics iO

Property Value SourceSpace group P 32 1 2 DepositorCell constantsa, b, c, α, β, γ

78.45Å 78.45Å 159.10Å90.00◦ 90.00◦ 120.00◦

Depositor

Resolution (Å)6.00 � 2.7514.95 � 2.60

DepositorEDS

% Data completeness(in resolution range)

97.9 (6.00-2.75)96.8 (14.95-2.60)

DepositorEDS

Rmerge 0.07 DepositorRsym (Not available) Depositor

< I/σ(I) > 1 3.46 (at 2.61Å) XtriageRe�nement program X-PLOR 3.1 Depositor

R, Rfree0.246 , 0.3250.238 , 0.314

DepositorDCC

Rfree test set 1696 re�ections (10.00%) wwPDB-VPWilson B-factor (Å2) 51.2 Xtriage

Anisotropy 0.194 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.45 , 106.7 EDS

L-test for twinning2 < |L| > = 0.49, < L2 > = 0.32 XtriageEstimated twinning fraction 0.057 for -h,-k,l Xtriage

Fo,Fc correlation 0.90 EDSTotal number of atoms 3158 wwPDB-VP

Average B, all atoms (Å2) 47.0 wwPDB-VP

Xtriage's analysis on translational NCS is as follows: The largest o�-origin peak in the Patterson

function is 3.64% of the height of the origin peak. No signi�cant pseudotranslation is detected.

1Intensities estimated from amplitudes.2Theoretical values of < |L| >, < L2 > for acentric re�ections are 0.5, 0.333 respectively for untwinned datasets,

and 0.375, 0.2 for perfectly twinned datasets.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#data_stats


5 Model quality iO

5.1 Standard geometry iO

Bond lengths and bond angles in the following residue types are not validated in this section:NAG

The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).

Mol ChainBond lengths Bond angles

RMSZ #|Z| >5 RMSZ #|Z| >51 A 0.77 0/1492 0.75 1/2035 (0.0%)2 B 0.75 2/1591 (0.1%) 0.75 2/2160 (0.1%)3 C 0.77 0/114 0.69 0/151All All 0.76 2/3197 (0.1%) 0.75 3/4346 (0.1%)

Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying ifthe center is modelled as a planar moiety or with the opposite hand.A planarity outlier is detectedby checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of asidechain that are expected to be planar.

Mol Chain #Chirality outliers #Planarity outliers1 A 0 1

All (2) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 B 87 GLU CD-OE2 7.57 1.33 1.252 B 31 PHE C-N -6.92 1.18 1.34

All (3) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 B 31 PHE O-C-N -6.28 112.66 122.701 A 174 LEU CA-CB-CG 5.11 127.05 115.302 B 28 ASP CB-CG-OD1 5.10 122.89 118.30

There are no chirality outliers.

All (1) planarity outliers are listed below:

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#model_quality

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#standard_geometry


Mol Chain Res Type Group1 A 150 TYR Sidechain

5.2 Too-close contacts iO

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes withinthe asymmetric unit, whereas Symm-Clashes lists symmetry related clashes.

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 1447 0 1387 62 02 B 1548 0 1462 79 03 C 113 0 128 10 04 A 28 0 26 3 05 A 8 0 0 1 05 B 13 0 0 1 05 C 1 0 0 0 0All All 3158 0 3003 136 0

The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 23.

All (136) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2Interatomicdistance (Å)

Clashoverlap (Å)

2:B:74:ARG:NH1 3:C:94:ALA:HB1 1.86 0.902:B:176:GLU:HG2 2:B:183:PRO:HB3 1.56 0.851:A:16:PRO:HG2 2:B:6:ARG:HA 1.58 0.842:B:74:ARG:HH11 3:C:94:ALA:HB1 1.39 0.831:A:8:ILE:HG23 1:A:25:ASP:HB3 1.60 0.832:B:31:PHE:CE2 2:B:36:GLU:HB2 2.15 0.812:B:180:VAL:HG11 2:B:184:LEU:HD11 1.64 0.791:A:15:ASN:HB2 1:A:70:LEU:HD21 1.64 0.792:B:71:LYS:HE3 3:C:97:LEU:HD13 1.67 0.751:A:71:GLU:O 1:A:75:LYS:HD3 1.88 0.732:B:27:LEU:HG 2:B:29:ARG:HD3 1.74 0.701:A:95:SER:HB2 1:A:96:PRO:HD2 1.74 0.694:A:181:NAG:C3 4:A:181:NAG:O7 2.42 0.682:B:50:VAL:HG23 2:B:51:THR:HG23 1.76 0.671:A:115:PRO:O 1:A:137:PHE:CE1 2.48 0.661:A:126:LYS:HD2 1:A:126:LYS:H 1.59 0.66

Continued on next page...

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#close_contacts


Continued from previous page...


Clashoverlap (Å)

1:A:8:ILE:HD11 1:A:10:ALA:HB2 1.76 0.664:A:181:NAG:H3 4:A:181:NAG:O7 1.96 0.662:B:82:ASN:O 2:B:86:VAL:HG22 1.96 0.651:A:15:ASN:CB 1:A:70:LEU:HD21 2.27 0.641:A:11:GLU:HA 1:A:21:GLU:O 1.97 0.641:A:176:LYS:HA 1:A:176:LYS:HE3 1.78 0.642:B:16:HIS:HB2 2:B:25:ARG:HB3 1.81 0.62

1:A:119:VAL:HG22 1:A:165:VAL:HG22 1.81 0.622:B:97:PRO:HB3 2:B:122:PHE:HB3 1.82 0.611:A:92:LEU:HD11 2:B:156:GLN:NE2 2.17 0.601:A:7:ILE:HG12 1:A:26:PHE:HD1 1.66 0.601:A:65:VAL:HG11 3:C:96:PRO:O 2.03 0.591:A:87:PRO:HB2 1:A:109:ILE:HG23 1.85 0.581:A:109:ILE:N 1:A:109:ILE:HD12 2.18 0.582:B:77:ASN:O 3:C:92:ARG:HD2 2.04 0.571:A:121:TRP:O 1:A:127:PRO:HA 2.04 0.572:B:13:SER:HB3 2:B:26:TYR:HE1 1.67 0.572:B:52:GLU:O 2:B:55:ARG:HG2 2.05 0.571:A:79:TYR:N 1:A:79:TYR:CD1 2.72 0.571:A:94:ASN:HB2 1:A:104:VAL:HB 1.87 0.571:A:105:LEU:HB3 1:A:121:TRP:CH2 2.40 0.561:A:92:LEU:HD11 2:B:156:GLN:HE22 1.70 0.562:B:62:ASN:HA 2:B:68:LEU:HD21 1.86 0.56

2:B:159:VAL:HG23 2:B:159:VAL:O 2.05 0.561:A:168:TRP:CZ2 2:B:6:ARG:NH2 2.74 0.562:B:163:THR:O 2:B:165:PRO:HD3 2.06 0.56

2:B:12:THR:HG22 2:B:14:GLU:HG3 1.88 0.562:B:87:GLU:HG3 2:B:91:VAL:HB 1.89 0.551:A:119:VAL:HB 1:A:149:HIS:CE1 2.42 0.542:B:134:ASN:OD1 2:B:169:GLU:HB2 2.08 0.541:A:14:LEU:CD2 1:A:116:VAL:HG23 2.38 0.542:B:71:LYS:NZ 2:B:74:ARG:NH1 2.55 0.541:A:47:GLU:O 1:A:51:PHE:HD1 1.90 0.542:B:68:LEU:O 2:B:72:ARG:HG3 2.07 0.54

2:B:24:VAL:HG11 2:B:79:CYS:HB3 1.90 0.531:A:61:ALA:O 1:A:64:ALA:HB3 2.08 0.53

2:B:116:VAL:HG22 2:B:160:MET:HG2 1.92 0.521:A:103:ASN:HB3 1:A:153:PHE:CE1 2.45 0.522:B:177:HIS:O 2:B:180:VAL:HG22 2.09 0.52

1:A:119:VAL:HG13 1:A:163:CYS:SG 2.50 0.512:B:81:HIS:CD2 3:C:92:ARG:HG3 2.44 0.51

Continued on next page...




Clashoverlap (Å)

2:B:122:PHE:HB2 2:B:177:HIS:NE2 2.25 0.512:B:28:ASP:HB3 2:B:40:PHE:HB3 1.92 0.511:A:115:PRO:O 1:A:137:PHE:CZ 2.63 0.512:B:29:ARG:HB2 2:B:31:PHE:HE1 1.76 0.511:A:23:MET:CE 1:A:25:ASP:HB2 2.41 0.501:A:38:LYS:NZ 1:A:38:LYS:HB2 2.26 0.50

1:A:137:PHE:CE1 1:A:147:LYS:HD2 2.47 0.491:A:14:LEU:HD13 2:B:8:LEU:HD13 1.94 0.491:A:117:VAL:CG1 1:A:118:ASN:N 2.75 0.492:B:17:PHE:HB3 2:B:20:GLY:O 2.12 0.492:B:69:GLU:HA 2:B:72:ARG:HB2 1.95 0.481:A:147:LYS:HE3 1:A:149:HIS:NE2 2.27 0.481:A:92:LEU:HG 1:A:93:THR:N 2.28 0.482:B:14:GLU:O 2:B:26:TYR:HA 2.13 0.48

2:B:172:THR:HG22 2:B:187:GLU:HG2 1.94 0.482:B:61:TRP:CG 3:C:97:LEU:HD23 2.49 0.482:B:144:SER:HB2 2:B:159:VAL:HG12 1.95 0.482:B:161:LEU:HD22 2:B:163:THR:OG1 2.14 0.481:A:79:TYR:N 1:A:79:TYR:HD1 2.12 0.47

2:B:129:VAL:CG1 2:B:159:VAL:HG21 2.44 0.472:B:131:TRP:NE1 2:B:161:LEU:HB2 2.29 0.472:B:41:ASP:HB3 2:B:44:VAL:HG23 1.96 0.471:A:67:LYS:O 1:A:70:LEU:HB3 2.14 0.47

1:A:91:VAL:HG21 1:A:176:LYS:O 2.15 0.472:B:29:ARG:NH1 2:B:29:ARG:HG3 2.30 0.472:B:144:SER:CB 2:B:159:VAL:HG12 2.46 0.462:B:55:ARG:N 2:B:56:PRO:CD 2.78 0.462:B:29:ARG:CB 2:B:31:PHE:CE1 2.98 0.462:B:49:ALA:HB2 2:B:55:ARG:HA 1.98 0.461:A:16:PRO:CG 2:B:6:ARG:HA 2.39 0.462:B:24:VAL:HB 2:B:75:VAL:HG13 1.98 0.462:B:141:GLY:O 2:B:162:GLU:HG2 2.16 0.45

2:B:129:VAL:HG13 2:B:175:VAL:HG22 1.99 0.452:B:71:LYS:CE 3:C:97:LEU:HD13 2.41 0.452:B:137:GLU:O 2:B:139:LYS:HG3 2.17 0.452:B:29:ARG:HB2 2:B:31:PHE:CE1 2.51 0.451:A:112:PHE:CE2 1:A:117:VAL:CG2 3.00 0.451:A:58:GLY:O 1:A:61:ALA:HB3 2.17 0.452:B:177:HIS:CG 2:B:178:PRO:HD2 2.52 0.451:A:5:HIS:ND1 1:A:26:PHE:CZ 2.85 0.45

1:A:117:VAL:HG12 1:A:118:ASN:N 2.31 0.44Continued on next page...




Clashoverlap (Å)

1:A:15:ASN:HB3 1:A:16:PRO:HD3 1.99 0.441:A:53:SER:O 3:C:90:LYS:HA 2.17 0.441:A:39:LYS:HD2 1:A:39:LYS:N 2.31 0.442:B:27:LEU:CG 2:B:29:ARG:HD3 2.45 0.431:A:34:VAL:HG21 1:A:59:ALA:HB2 1.99 0.431:A:23:MET:HE2 1:A:25:ASP:HB2 2.00 0.432:B:67:LEU:O 2:B:70:GLN:HB3 2.18 0.43

1:A:118:ASN:OD1 4:A:200:NAG:C7 2.66 0.432:B:71:LYS:HZ1 2:B:74:ARG:HH12 1.66 0.432:B:174:GLN:OE1 2:B:185:THR:HB 2.18 0.432:B:97:PRO:HA 2:B:120:SER:O 2.18 0.431:A:115:PRO:HG3 1:A:145:PHE:CE2 2.54 0.432:B:58:ALA:O 2:B:62:ASN:ND2 2.52 0.43

2:B:94:ARG:NH2 5:B:198:HOH:O 2.51 0.432:B:33:ASN:C 2:B:34:GLN:HG3 2.38 0.42

1:A:109:ILE:HG22 1:A:112:PHE:CE1 2.54 0.422:B:127:ILE:HG12 2:B:128:GLU:N 2.34 0.422:B:71:LYS:HZ3 2:B:74:ARG:NH1 2.17 0.421:A:108:PHE:HE1 1:A:146:ARG:HB3 1.85 0.422:B:71:LYS:NZ 2:B:74:ARG:HH12 2.17 0.42

1:A:45:LEU:HD12 1:A:48:PHE:CZ 2.54 0.421:A:133:SER:HB2 1:A:150:TYR:HB2 2.02 0.422:B:39:ARG:HG3 2:B:39:ARG:O 2.20 0.421:A:96:PRO:HA 5:A:204:HOH:O 2.20 0.411:A:135:THR:O 1:A:147:LYS:NZ 2.48 0.412:B:13:SER:HB3 2:B:26:TYR:CE1 2.52 0.412:B:29:ARG:HB3 2:B:31:PHE:CE1 2.55 0.412:B:31:PHE:CD2 2:B:36:GLU:HB2 2.54 0.412:B:28:ASP:O 2:B:39:ARG:HA 2.21 0.412:B:66:ASP:O 2:B:70:GLN:HB2 2.20 0.412:B:81:HIS:O 2:B:85:VAL:HG23 2.21 0.41

1:A:164:ARG:HH22 1:A:166:GLU:CD 2.24 0.411:A:26:PHE:CD2 2:B:90:THR:HB 2.55 0.412:B:127:ILE:HG12 2:B:128:GLU:H 1.85 0.411:A:111:LYS:HG2 1:A:140:ARG:CZ 2.51 0.401:A:161:TYR:O 1:A:178:TRP:N 2.53 0.402:B:166:ARG:O 2:B:169:GLU:HG2 2.22 0.402:B:81:HIS:HD2 3:C:92:ARG:HG3 1.87 0.40

There are no symmetry-related clashes.


5.3 Torsion angles iO

5.3.1 Protein backbone iO

In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all X-ray entries followed by that with respect to entriesof similar resolution.

The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 174/176 (99%) 150 (86%) 23 (13%) 1 (1%) 25 42

2 B 185/187 (99%) 159 (86%) 22 (12%) 4 (2%) 6 11

3 C 13/15 (87%) 13 (100%) 0 0 100 100

All All 372/378 (98%) 322 (87%) 45 (12%) 5 (1%) 12 21

All (5) Ramachandran outliers are listed below:

Mol Chain Res Type2 B 138 GLU2 B 167 SER2 B 168 GLY2 B 112 HIS1 A 171 ASP

5.3.2 Protein sidechains iO

In the following table, the Percentiles column shows the percent sidechain outliers of the chain as apercentile score with respect to all X-ray entries followed by that with respect to entries of similarresolution.

The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 161/161 (100%) 148 (92%) 13 (8%) 11 21

2 B 172/172 (100%) 162 (94%) 10 (6%) 20 35

3 C 13/13 (100%) 13 (100%) 0 100 100

All All 346/346 (100%) 323 (93%) 23 (7%) 16 29

All (23) residues with a non-rotameric sidechain are listed below:

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#torsion_angles

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#protein_backbone

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#protein_sidechains


Mol Chain Res Type1 A 8 ILE1 A 39 LYS1 A 50 ARG1 A 79 TYR1 A 83 THR1 A 92 LEU1 A 113 THR1 A 126 LYS1 A 128 VAL1 A 171 ASP1 A 172 GLU1 A 174 LEU1 A 176 LYS2 B 21 THR2 B 38 VAL2 B 88 SER2 B 96 HIS2 B 112 HIS2 B 131 TRP2 B 138 GLU2 B 140 THR2 B 161 LEU2 B 185 THR

Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (6) suchsidechains are listed below:

Mol Chain Res Type1 A 15 ASN2 B 16 HIS2 B 37 ASN2 B 77 ASN2 B 81 HIS2 B 112 HIS

5.3.3 RNA iO

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains iO

There are no non-standard protein/DNA/RNA residues in this entry.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#rna

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#nonstandard_residues_and_ligands


5.5 Carbohydrates iO

There are no monosaccharides in this entry.

5.6 Ligand geometry iO

2 ligands are modelled in this entry.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are de�ned in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res LinkBond lengths Bond angles

Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

4 NAG A 200 1 14,14,15 0.77 1 (7%) 17,19,21 0.76 04 NAG A 181 1 14,14,15 0.56 0 17,19,21 0.68 0

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number de�ned in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.'-' means no outliers of that kind were identi�ed.

Mol Type Chain Res Link Chirals Torsions Rings4 NAG A 200 1 - 0/6/23/26 0/1/1/14 NAG A 181 1 - 3/6/23/26 0/1/1/1

All (1) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)4 A 200 NAG C1-C2 2.28 1.55 1.52

There are no bond angle outliers.

There are no chirality outliers.

All (3) torsion outliers are listed below:

Mol Chain Res Type Atoms4 A 181 NAG C3-C2-N2-C74 A 181 NAG O5-C5-C6-O64 A 181 NAG C4-C5-C6-O6




There are no ring outliers.

2 monomers are involved in 3 short contacts:

Mol Chain Res Type Clashes Symm-Clashes4 A 200 NAG 1 04 A 181 NAG 2 0

5.7 Other polymers iO

There are no such residues in this entry.

5.8 Polymer linkage issues iO

The following chains have linkage breaks:

Mol Chain Number of breaks2 B 1

All chain breaks are listed below:

Model Chain Residue-1 Atom-1 Residue-2 Atom-2 Distance (Å)1 B 31:PHE C 32:HIS N 1.18


https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#polymer_linkage


6 Fit of model and data iO

6.1 Protein, DNA and RNA chains iO

In the following table, the column labelled `#RSRZ> 2' contains the number (and percentage)of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative toall X-ray entries and entries of similar resolution. The OWAB column contains the minimum,median, 95th percentile and maximum values of the occupancy-weighted average B-factor perresidue. The column labelled `Q< 0.9' lists the number of (and percentage) of residues with anaverage occupancy less than 0.9.

Mol Chain Analysed <RSRZ> #RSRZ>2 OWAB(Å2) Q<0.9

1 A 176/176 (100%) 0.15 11 (6%) 20 24 15, 42, 73, 85 1 (0%)

2 B 187/187 (100%) 0.33 11 (5%) 22 27 22, 46, 81, 85 14 (7%)

3 C 15/15 (100%) -0.03 1 (6%) 17 21 22, 41, 69, 71 0

All All 378/378 (100%) 0.23 23 (6%) 21 26 15, 44, 78, 85 15 (3%)

All (23) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ2 B 109 LEU 5.91 A 100 ARG 5.02 B 18 PHE 3.82 B 106 THR 3.72 B 108 PRO 3.62 B 107 GLN 3.11 A 130 THR 2.82 B 167 SER 2.82 B 105 LYS 2.81 A 163 CYS 2.52 B 170 VAL 2.53 C 87 PRO 2.41 A 171 ASP 2.31 A 141 GLU 2.31 A 180 PHE 2.21 A 101 GLU 2.21 A 126 LYS 2.21 A 129 THR 2.21 A 38 LYS 2.12 B 19 ASN 2.11 A 172 GLU 2.12 B 112 HIS 2.12 B 134 ASN 2.0

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_model_data

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_protein_na_chains


6.2 Non-standard residues in protein, DNA, RNA chains iO

There are no non-standard protein/DNA/RNA residues in this entry.

6.3 Carbohydrates iO

There are no monosaccharides in this entry.

6.4 Ligands iO

In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber de�ned in the chemical component dictionary. The B-factors column lists the minimum,median, 95th percentile and maximum values of B factors of atoms in the group. The columnlabelled `Q< 0.9' lists the number of atoms with occupancy less than 0.9.

Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.94 NAG A 200 14/15 0.53 0.47 85,86,88,88 04 NAG A 181 14/15 0.78 0.44 74,77,79,79 0

6.5 Other polymers iO

There are no such residues in this entry.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_nonstandard_and_ligands




full wwpdb x-ray structure validation report i · ramachandranoutliers 120053 1013(2.78-2.74)...

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